Research workbench
Crystal structure of the glycosyltransferase snogd from streptomyces nogalater
Analyse Crystal structure of the glycosyltransferase snogd from streptomyces nogalater in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AN4
- Type
- protein
- Length
- 1,393 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl transferase
- UniProt
- Q9RN61
- Ligands
- DUD
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl transferase | protein | 358 | 41% helix, 17% strand | Q9RN61 |
| B | Glycosyl transferase | protein | 359 | 42% helix, 16% strand | Q9RN61 |
| C | Glycosyl transferase | protein | 328 | 40% helix, 18% strand | Q9RN61 |
| D | Glycosyl transferase | protein | 348 | 41% helix, 16% strand | Q9RN61 |
Ligands and binding sites
- DUD · Deoxyuridine-5'-diphosphate · ligand · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.74 | 0.87 | 39 | empty |
| 2 | 273 | 0.74 | 0.88 | 35 | empty |
| 3 | 347 | 0.72 | 0.85 | 44 | empty |
| 4 | 283 | 0.72 | 0.86 | 40 | empty |
| 5 | 354 | 0.68 | 0.82 | 39 | DUD |
Interfaces
5 interfaces between chains.
- A–B · 1554 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1496 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 872 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 63 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 4AN4 · Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9RN61
- Elsewhere: RCSB PDB 4AN4 · PDBe 4AN4 · UniProt Q9RN61
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